Help with picking out new audio equipment

The most important speakers are the dash speakers. I don't see them on your list. The least important speakers are the rear door speakers.
I didn't check the price of all the parts you suggested, but i think you are spending far too much money on speakers.
For example, the Infinity kappa 60.11 are $350 at crutchfield. They are also 2 ohm speakers. Infinity often rates their efficiency of their 2 ohm speakers at 2 watts, rather than 1 watt. Specifically, they rat them at 2.82 volts. If that is true for these speakers, then they are really 90db efficient, which isn't bad, but you can do better. You can get decent front door speakers for $50 - $100 a pair. My dash speakers cost about $35 a pair.

I really think it more important to have a dsp processor that equalizes the frequency response of your speakers, such as the jbl-ms8 amp I used.
It is $455 at amazon, vs $262 and has less power per channel, but it has 8 channels. I was driving home today, and using 8 channels, it had more than enough power for me. I really think people go overboard on power for car stereo's. Except for really low frequencies, if you are using reasonably efficient speakers, not much power is needed. Unless you like playing pipe organ music (like I do), most music doesn't have a lot of really low end frequencies. I have a 75w 2 channel amp I could use for my subwoofers, but the two 20w channels of the ms-8 is enough for me. I do have an efficient sub, with pretty efficient drivers though.

See Lopgok's stereo upgrade - in many small parts | PriusChat for all the gory details.

 

Save some money & skip the rear speakers. The front should be plenty. To try it out, turn your fader all the way to the front. You should hear your "sound stage" moving to the front.

If you go with a "passive system" such as most of the speakers you mention above, they will have a crossover included. I'm not familiar with the amp, but you may need a line output converter (LOC) to step down the speaker output from the factory head unit. I also am choosing to go with a DSP. It replaces the crossovers and should replace the LOC as well. It adds much more tuning, but complexity as well.

I'm not going to open the debate, but there are other threads talking about whether or not you can or should install an amp and what size. There are plenty of examples that show you can without ill effect.

I have slowly been piecing mine together and have about $900 in the following so far:

• Precision Power DEQ.8 processor - $350
  
• Alpine PDX V9 5 channel amp -$250 (used)
  
• Dayton Audio RS180-4P 7" Reference Woofer 4 Ohm - $88.18
  
• Dayton Audio RS28F-4 1-1/8" Silk Dome Tweeter - $93.29
  
• Dayton Audio RSS265HO-4 10" Reference HO Subwoofer 4 Ohm - $115.02

The DSP came in today. I just need to get some MLV and CCF for sound deadoning and I can start the install.

 

I have plenty of MLV for sale cheap. Too bad I am not close enough for you to pick it up.
You don't have to wait for MLV to start your install. You can add it any time. If you will be lifting up the carpets to do the
floor, then you definitely want to put in the MLV and CCF at that time, because it is a big hassle to lift the carpet. For the doors, it just takes a minute or two to pull them off. I have yet to install my MLV and CCF in my doors. The ceiling will be next, but I want to know more about how to remove it without breaking anything...

 

You could put the tweeters in the dash location. The dash location is the best location for speakers in the car. The door speakers are great if you had ears in your ankles, which I presume you don't. When I was using the factory amp, I put in speakers in one location at a time. The door speakers did a bit, but not much. The dash speakers have pretty much a direct shot to your ears. I used the polk
Polk Audio DXi350 3-1/2" 2-way car speakers at Crutchfield.com
speakers. I also added a big bass blocking cap to allow low frequencies to get through. I removed the cap when I ran wires for the JBL MS-8 amplifier. Right now, with my MS-8 amp, I have them cut off at 100hz. I suspect they could use cutting off a bit higher, perhaps 200hz, but the MS-8 isn't flexible enough for that (or I haven't figured out how to do it). A real tweeter will go down to 1 or 2khz. You want a lot of lower frequencies to get through if possible for your dash speaker.

As for wiring kit, I just wired it up. I bought all the wire and connectors I would need, and I bought a good ratcheting crimp tool to make good connections. You will have to tap into the speaker outputs if you keep your head unit. I tapped into them at the front door junction. I ran wires from all of the speakers to under the passenger seat area. I used 8 gauge wiring from the battery to under the seat. I ran a separate 12v wire in case I wanted a bigger subwoofer amp, which I didn't use. I also ran my subwoofer wires back to the trunk area when I was running the 12v wires. I used maxi-blade fuses which have much better connectors than the 'pro audio' round connectors. I ran a big ground wire from the battery to the chassis. You can see all of this on my priuschat post. All of this can be bought locally, or online. Some ring terminals and the maxi-fuses I bought on ebay. I doubt any 'kit' will fit your prius properly.

You might want to check out my subwoofer; it is at the bottom of my priuschat post I referenced in my earlier posting.
I suspect it sounds better than almost any other prius subwoofer.

 

The JBL MS-8 *is* an 8 channel 20 watt rms amp (at 4 ohms) and 30 watts rms at 2 ohms, as well as a DSP.
It also has line-level outputs so you can use any of its 8 channels with an external amplifier.
From what I could tell the DSP-88R doesn't have microphones to auto-calibrate the DSP.
Using the supplied microphones for the JBL MS-8 makes it really quick and easy to calibrate...

I think it is a better path than your original path. Likely less expensive, more flexible and will sound better.

 

I wouldn't have the toyota dealer install the MS-8. I think they are unfamiliar with it, and will likely charge too much. Either do it yourself, or go to a decent car audio place. They will likely be more familiar with the unit and likely do a better install.

I went around the vapor barrier at first. Then I covered it on my second pass with sound deadening material. If I was doing it over, I would cover the panels with aluminum flashing either glued or screwed on. Then I would cover the flashing with sound deadening. I think it is a bad idea to leave it alone, as it will flap with low frequencies. It is not like doors are ideal speaker enclosures at all, but the flapping can't do any good. If I need to access the door, I will have to cut the sound deadening material, which is workable.

For speaker adapters do not buy the crutchfield 12x12 plastic. I have some and it is for sale. There are several problems. First it is a hassle to cut to the right shape. Second it is flat, and you want the speaker to stick out about 1/2 an inch.Buy the metra adapters, which are available on ebay. No idea why crutchfield doesn't stock them. You want METRA 82-8146. I wrote it up at weasel.com: 2012 Toyota Plug in Prius Stereo but I didn't put those details on priuschat.com

You don't want to cut the factory connectors, just the wire reasonably close to them. For the front door speakers, it is easy. For the rear door speakers, the color coding was screwy on the drivers side, but really easy to deal with on the passenger side. For the dash speakers, I just ran wires directly from them, and ignored the factory wiring. I recommend using 16 gauge wiring. I ended uo running out of a 50 foot roll and ended up with 18 gauge for my rear doors. I really don't see the need for thicker wire unless you plan on a really big amp. There will be a lot of wires under the carpet, and thicker wires will be more bulky. Don't forget to run front speaker outputs from the head unit. the amplifier will need them. 18 gauge is plenty for them, as they will not be carrying any current. I used a different colored wire in my build to make them stand out. As for getting the polarity correct, toyota has documented colors for + and - for all of their wiring. Every aftermarket speaker you buy will have the + and - labelled. I soldiered all of my speaker wires, and covered them with heatshirnk. it is less bulky than a crimp connector. I used crimp connectors for the + and - power for the amp, and the 1/4 spade connectors for my woofer.

If you do use component speakers, remember there are only 8 channels on the MS-8. As long as you don't run out of channels, you don't need to use the passive crossovers. I really think the dash speaker is the most critical and I think just a tweeter there won't be ideal. I find it curious that almost all the 'component' speakers are 2 way. The midrange frequencies are the most critical for listening. A 2 way system will have a tweeter and a woofer. I don't think my $50 kenwood 3 way speakers will have great midrange or a sophisticated crossover, but at least they have a midrange driver.

If you do your install, be sure to get all the right sized connectors. It took me a few iterations to get all the right connectors, which caused some delays.